From chemistry-request@server.ccl.net Fri Nov 8 04:17:37 2002 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA89HaQ21396 for ; Fri, 8 Nov 2002 04:17:36 -0500 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id gA89T6115713 for ; Fri, 8 Nov 2002 17:29:11 +0800 Date: Fri, 8 Nov 2002 17:29:06 +0800 (HKT) From: Hu LiHong To: chemistry@ccl.net Subject: AUTODOCK Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I found if I import the same ligand with different coordinate, different Final Docked Energy will be got. Is it normal? What is the reason for this, Is something wrong with my Autodock program? Thank you in advance, Best regards, Carol From chemistry-request@server.ccl.net Fri Nov 8 02:58:14 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA87wDQ19659 for ; Fri, 8 Nov 2002 02:58:14 -0500 Received: from chemie.uni-erlangen.de (equinox.chemie.uni-erlangen.de [131.188.128.90]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id IAA01073 for ; Fri, 8 Nov 2002 08:58:13 +0100 (MET) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3DCB6EBA.86DBBCF@chemie.uni-erlangen.de> Date: Fri, 08 Nov 2002 08:58:50 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Free Protein Builder References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mark Zottola - Contractor wrote: > > I am looking for freeware (or shareware) which can reasonably build protein > motifs. That is, I want to build a peptide sequence which has certain > residues in an alpha-helical arrangement followed by say extended > conformation, etc. I have a secondary structure prediction of a peptide > sequence and want to examine families of tertiary structures based on that > secondary structure prediction. > Dear Mark, there are several programs that can do that - e.g. the protein module within the TINKER package allows explicit secondary structure definition upon building the peptide chain or DeepView (was SPDBV), which allows loading an existing pdb file and interactive altering of the secondary structure or selected areas. Both are non-commercial... Hope that helps, -Harry > Two dogpile searches failed to turn up anything. So I would be very > grateful for any pointers to some useful software. > > Thanks! > ***************************************************************** > Dr. Mark A. Zottola > PET Director of Computational Chemistry and Materials > Army Research Laboratory MSRC > PB 191 939-I Beards Hill Road > Aberdeen MD 21001 > VOICE: 410 278 7250 FAX: 410 297 9521 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen oder Lehrstuhl fuer Schuhstrasse 19 Pharmazeutische Chemie D-91052 Erlangen, Germany Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Nov 7 18:58:43 2002 Received: from sandmail01.sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA7NwcC08741 for ; Thu, 7 Nov 2002 18:58:39 -0500 To: chminf-l@listserv.indiana.edu, chemistry@server.ccl.net Cc: qsar_society@accelrys.com Subject: Call for papers - Informatics Challenges in Pharmacogenomics MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: osman@accelrys.com Date: Thu, 7 Nov 2002 15:58:34 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 11/07/2002 03:58:42 PM, Serialize complete at 11/07/2002 03:58:42 PM Content-Type: multipart/alternative; boundary="=_alternative 0083918288256C6A_=" This is a multipart message in MIME format. --=_alternative 0083918288256C6A_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable INFORMATIC CHALLENGES IN PHARMACOGENOMICS At Spring ACS meeting in New Orleans (March 23-27, 2003) Sponsored by the Biotechnology Secretariat (BTEC) Co-sponsored by Chemical Information Division (CINF) and Co-sponsored by Division of Medicinal Chemistry (MEDI) New fields providing new challenges in informatics. How do we capture the = dataflow from pharmacogenomics research and how do we manage this=20 information?=20 Please use the OASYS to submit your abstract. You can access the BTEC=20 symposia at OASYS via http://oasys.acs.org/acs/225nm/btec/papers/ . The=20 deadline for submitting abstracts is November 22nd. Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman@accelrys.com, http://www.accelrys.com --=_alternative 0083918288256C6A_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
INFORMATIC CHALLENGES IN PHARMACOGEN= OMICS

At Spring ACS meeting in New Orleans= (March 23-27, 2003)

Sponsored by the Biotechnology Secre= tariat (BTEC)
Co-sponsored by Chemical Information= Division (CINF) and
Co-sponsored by Division of Medicina= l Chemistry (MEDI)

New fields providing new challenges = in informatics.  How do we capture the dataflow from pharmacogenomics = research and how do we manage this information?  

Please use the OASYS to submit your = abstract. You can access the BTEC symposia at OASYS via http://oasys.acs.or= g/acs/225nm/btec/papers/ . The deadline for submitting abstracts is Novembe= r 22nd.

Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman@accelrys.com, http://www.accelrys.com --=_alternative 0083918288256C6A_=-- From chemistry-request@server.ccl.net Fri Nov 8 03:36:18 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA88aHQ20316 for ; Fri, 8 Nov 2002 03:36:17 -0500 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id gA88Z3dX030221; Fri, 8 Nov 2002 09:35:03 +0100 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id gA88Z2lN030218; Fri, 8 Nov 2002 09:35:03 +0100 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Fri, 8 Nov 2002 09:35:02 +0100 (CET) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: Mark Zottola - Contractor cc: CHEMISTRY@ccl.net Subject: Re: CCL:Free Protein Builder In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gA88aIQ20317 Hi, I think that one of the best free protein builder is The Swiss PDB Viewer downloadable at http://www.expasy.org/spdbv/ Best Reguards Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Thu, 7 Nov 2002, Mark Zottola - Contractor wrote: > I am looking for freeware (or shareware) which can reasonably build protein > motifs. That is, I want to build a peptide sequence which has certain > residues in an alpha-helical arrangement followed by say extended > conformation, etc. I have a secondary structure prediction of a peptide > sequence and want to examine families of tertiary structures based on that > secondary structure prediction. > > Two dogpile searches failed to turn up anything. So I would be very > grateful for any pointers to some useful software. > > Thanks! > ***************************************************************** > Dr. Mark A. Zottola > PET Director of Computational Chemistry and Materials > Army Research Laboratory MSRC > PB 191 939-I Beards Hill Road > Aberdeen MD 21001 > VOICE: 410 278 7250 FAX: 410 297 9521 > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Nov 7 21:07:45 2002 Received: from web12802.mail.yahoo.com ([216.136.174.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gA827jC11750 for ; Thu, 7 Nov 2002 21:07:45 -0500 Message-ID: <20021108020745.40161.qmail@web12802.mail.yahoo.com> Received: from [210.14.43.25] by web12802.mail.yahoo.com via HTTP; Thu, 07 Nov 2002 18:07:45 PST Date: Thu, 7 Nov 2002 18:07:45 -0800 (PST) From: amor san juan Subject: Re: CCL:Autodock To: "Pandey, Jaya" , chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Jaya! If your goal is to view your docking output, you can use Autodock tools (ADT) available MGL lab at scripps website: http://www.scripps.edu/~sanner/python/index.html Also, I suggest you read the PMV tutorial to guide you effectively in using ADT. Finesse, Amor --- "Pandey, Jaya" wrote: > Dear All, > > I am trying to use autodock to generate some > inhibitors for my receptor. I > work in UNIX and do not visualise the proceedings of > the docking. Is there a > program that has a window to visualise like VEGA the > proceedings of the > auotdocking steps?? Please reply and help as I am > not really able to > understand and move on much. > > Thanks > > jaya > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2 From chemistry-request@server.ccl.net Fri Nov 8 13:14:23 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA8IENQ07470 for ; Fri, 8 Nov 2002 13:14:23 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id NAA05997 for ; Fri, 8 Nov 2002 13:14:12 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DCBFEF5.39A4EF95@cornell.edu> Date: Fri, 08 Nov 2002 13:14:13 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Questions about SCF convergence again with Gaussian98W and Hyperchem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone -- thank you for all your good suggestions... I'm still having trouble getting an optimization and frequency calculation to work for a charged molecule with 120 atoms. I've tried with both Hyperchem and Gaussian98W using the PM3 method. And I've tried some fo the suggestions given by listmembers such as increasing the maximum number of iterations to 500, setting scf=sleazy, setting scf=qc, etc... I still get the UNABLE TO ACHIEVE SELF CONSISTENCE error after (at most) one optimization step. So the energy will converge once, it moves the atoms by a little bit for the optimization and the energy fails to converge. I have the same problem with hyperchem. Hyperchem does the neutral case just fine, but as soon as I add a charge of -1 and a multiplicity of 2, the energy does not even get close to something reasonable (it's large and positive). Does anyone have any further suggestions on what I can do to get either of the programs to work? Hyperchem does work for a smaller molecule (~70 atoms), but Gaussian does not. Does the size of the molecule make it more difficult for these programs and methods to find the minimum energy? I tried a charged water molecule in Gaussian and it worked fine.... thanks. Connie From chemistry-request@server.ccl.net Fri Nov 8 13:14:13 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id gA8IEDE07447 for chemistry@ccl.net; Fri, 8 Nov 2002 13:14:13 -0500 Message-ID: <20021108160230.28406.qmail@linuxmail.org> From: "Bimo Ario Tejo" To: chemistry@ccl.net Cc: jkl@ccl.net Date: Fri, 08 Nov 2002 18:02:30 +0200 Subject: residue cross-correlation Dear CCLers, I'd like to know any modelling package which can analyse residue cross-correlation over an MD trajectory. I have some AMBER trajectories but I have't got any response from Amber community until now. I hope somebody can help me since I *really* need this analysis tool. Best regards, Bimo -- ______________________________________________ http://www.linuxmail.org/ Now with POP3/IMAP access for only US$19.95/yr Powered by Outblaze From chemistry-request@server.ccl.net Fri Nov 8 23:07:35 2002 Received: from trivial.uchicago.edu ([128.135.160.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA947YQ20533 for ; Fri, 8 Nov 2002 23:07:34 -0500 Received: from localhost (cmtaylor@localhost) by trivial.uchicago.edu (8.9.3/8.9.3) with ESMTP id WAA04791 for ; Fri, 8 Nov 2002 22:07:34 -0600 Date: Fri, 8 Nov 2002 22:07:34 -0600 (CST) From: Caroline Taylor To: CCL list Subject: converting MO's (coef) from gamess to gaussian order (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone. I was wondering if anyone had written a script to resort the MO coeficients from a GAMESS job into the correct order for input with cards in Gaussian? Thanks for your help!!! -Caroline -- --------------------------------------------- Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 http://home.uchicago.edu/~cmtaylor ---------------------------------------------